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https://github.com/jhu99/netcoffee

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https://github.com/jhu99/netcoffee

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README 

        
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PROGRAM: NetCoffee

AUTHOR: JIALU HU

EMAIL: [email protected]



Copyright (C) <2013>  



This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.



This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.



You should have received a copy of the GNU General Public License

along with this program.  If not, see .



################################################################################

Description

This file is README file of the package of NetCoffee, developed by Jialu Hu.

To guide you quickly starting to use our alignment tool, we structured this README into four parts:

1) PREREQUISITE

2) COMPILING

3) OPTION

4) EXAMPLE 

Before running this program, you are strongly recommended to read this file carefully.



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PREREQUISITE

1. LEMON Graph Library 1.2.3

The source code is freely available under Boost Software License, Version 1.0 at the website: http://lemon.cs.elte.hu/trac/lemon/wiki/Downloads

Please first compile the lemon graph library before compiling the code of NetCoffee.

Note that this package should move to the directory $NETCOFFEE/include.

2. FSST package

This package is necessary only if you want to use "-analyse" option to calculate the semantic similarities.

It can be download at http://gotax.bioinf.mpi-inf.mpg.de/avail.php.

3. GoTermFinder

This package is necessary only if you want to use "-analyse" option to draw the GoTree View or calculate p-Value of each match-set.

It can be download at http://search.cpan.org/dist/GO-TermFinder/lib/GO/TermFinder.pm.



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COMPILING

To compile the source code, the latest compilers which supports the standard language C++11, also known as C++0x, is needed. Other older compiler may not support it.

1. Compile LEMON GRAPH LIBRARY



cd $NETCOFFEE/include/lemon-1.2.3/

./configure

./make



2. Compile NetCoffee



cd $NETCOFFEE

./make MODE=Release

#If you want to compile it in Debug mode, run command:

./make (MODE=Debug)



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OPTION

You can see the detailed option information with option "-h".

It is noted that there are two options you must specify if you want to run NetCoffee for an alignment task. They are described as follows:



1. -profile

The default file is "./profile.input", but you can also change the filename and path by "-profile" option.

This file tells the program where to find the dataset and to create output files.

It is expected to be in two-column tab-delimited format.

These lines starting with "#" will be seen as comment.

Each line has one keyword and one value, like this:

$keyword	$value

Using this file, you are allowed to set options (network,gofile,efile,alignmentfile,avefunsimfile,scorefile,logfile) here.

However, you are also allowed to set these option in command line, except for these keywords: network, gofile, efile, which containing multiple files.

Note that, the values must be strictly in order from up to down for keywords "network, gofile, efile".

For example, suppose we have

three PPI networ:1.tab, 2.tab, 3.tab,

go association file: 1.fsst, 2.fsst, 3.fsst,

six balst evalue (or bitscore) files: 1-1.cf, 1-2.cf,...,3-3.cf,

then the profile should looks like:



--------------BEGIN OF PROFILE--------------

#COMMENT $keyword	$value

network  ./dataset/1.tab

network  ./dataset/2.tab

network  ./dataset/3.tab

gofile  ./dataset/goa/1.fsst

gofile  ./dataset/goa/2.fsst

gofile  ./dataset/goa/3.fsst

efile  ./dataset/1-1.cf

efile  ./dataset/1-2.cf

efile  ./dataset/1-3.cf

efile  ./dataset/2-2.cf

efile  ./dataset/2-3.cf

efile  ./dataset/3-3.cf

scorefile     ./dataset/score_composit.model

alignmentfile ./result/alignment_netcoffee.data

avefunsimfile netcoffee_fsst.result

logfile       ./result/measure_time.txt

--------------END OF PROFILE--------------



2. -scorefile

The default file is "./dataset/score_composit.model". This file was empirically obtained from blastp scoring files for othologous model and null model based on e-value.

If the option "bscore" was enabled, this file should be "./dataset/score_composit.bmodel", which calculates the sequence-based score based on bitscore. 

You can run commandline with option "-record -task 0" to generate this data with blastp scoring files.



3. -network

This option specifies the compared PPI networks, which is formated as follows:

--------------BEGIN OF NETWORK--------------

INTERACTOR_A	INTERACTOR_B

Q6QNY1	Q9NWB7

Q96P48	O00220

Q96P48	O14763

O15105	Q92905

Q92905	Q13485

Q16666	Q86WV6

Q9NZH6	P84022

P26717	O43914

P04234	P07766

--------------END OF NETWORK--------------



4. -efile

This option specifies the blastp sequence similarity files for each pair of species, which includes three columns seperated by .

The first column provides proteins from the first netwoks, the second column provides proteins from the second networks, the third column provides evalue or bitscore.

However, the options "-bscore" and "-scorefile ./dataset/score_composit.bmodel" must be used if the third column gives bitscore;

The change of protein order in the same line is not allowed.

There are two examples:



--------------BEGIN OF EVALUE FILE--------------

P31946	P62258	1e-116

P31946	Q04917	7e-133

P31946	P61981	2e-135

P31946	P31947	3e-122

P31946	P27348	2e-152

P31946	P63104	4e-162

P62258	P31946	1e-116

P62258	P62258	 0e+00

P62258	Q04917	4e-110

P62258	P61981	3e-112

--------------END OF EVALUE FILE--------------



--------------BEGIN OF BITSCORE FILE--------------

P31946	P62258	  325.0

P31946	Q04917	  367.0

P31946	P61981	  373.0

P31946	P31947	  340.0

P31946	P27348	  416.0

P31946	P63104	  441.0

P62258	P31946	  325.0

P62258	P62258	  524.0

P62258	Q04917	  309.0

P62258	P61981	  315.0

--------------END OF BITSCORE FILE--------------



5. other option in Usage



You can generate the following message by running the program with option "-h".



$NETCOFFEE/bin/netcoffee -h

Usage:

  ./bin/netcoffee -version|-records|-alignment|-analyse|-format

     [--help|-h|-help] [-alignmentfile str] [-alpha num] [-avefunsimfile str]

     [-beta num] [-bscore] [-distributionfile str] [-edgefactor num]

     [-eta num] [-formatfile str] [-nmax int] [-numspecies int]

     [-numthreads int] [-orthologyfile str] [-out] [-randomfile str]

     [-recordsfile str] [-resultfolder str] [-task int]

Where:

  --help|-h|-help

     Print a short help message

  -alignment

     Execute the alignment algorithm.

  -alignmentfile str

     The filename of alignment which is required to either create or analyse.

  -alpha num

     Prameter controlling how much topology score contributes to the alignment score. Default is 0.5.

  -analyse

     Make analysis on alignmenr result.

  -avefunsimfile str

     The filename for functional similarity of alignment.

  -beta num

     Probability for randomly picking out the alignment records. Default is 1.0

  -bscore

     Use bitscore as the similarity of edges.

  -distributionfile str

     Output file for log ratio distribution.

  -edgefactor num

     The factor of the power law normalization. Default is 0.1.

  -eta num

     Threshold imfactor which is used to exclude match-sets from a single species. Default is 1.0.

  -format

     Process input or output file into proper format.

  -formatfile str

     Profile of input parameters.

  -nmax int

     The parameter for SA algorithm N.

  -numspecies int

     Number of the species compared. Default is 4.

  -numthreads int

     Number of threads running in parallel.

  -orthologyfile str

     Training data for orthology model.

  -out

     Print the alignment result into file.

  -randomfile str

     Training data for random model.

  -records

     Generate alignment records file.

  -recordsfile str

     Records file for writing and reading. It is used to store the triplet edges.

  -resultfolder str

     The folder which was used as active folder in the data process.

  -task int

     Complete different tasks. The task was determined with other options such as -alignment together. Default is 1.

  -version

     Show the version number.



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EXAMPLE

1. Download dataset

Our datasets are freely available at our website: https://code.google.com/p/netcoffee/downloads/list.

Download it into the folder of $NETCOFFEE and uncompress it with command:

tar -zxvf dataset.tar.gz

2. Compile source code

Compile the source code with command:

make MODE=Release

3. Run NetCoffee on our test dataset-2 with command:

./bin/netcoffee -alignment -task 1 -out -alpha ${ALPHA} -numspecies ${num} -numthreads ${thread num} -alignmentfile ./result/alignment_netcoffee.data -resultfolder ./result/

${ALPHA} is the parameter you want to specify for alpha.

Then you can find the all the involved output files in ./result/ .

There are many other functions which you can see with "-help" option.



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END

THANKS FOR READING

If you have any questions regarding to the program, please don't hesitate to contact us through email.